About me and my work

Learning objectives

• Be able to share reproducible code for more scientific and transparent transport research
• To be confident reproducing your own work and that of others
• To become skilled at using Git and GitHub to manage versions of your code and collaborate with others
• To be able to write reproducible content that can be exported to a variety of formats with the Quarto system for scientific publishing
• To understand how Quarto extensions can be used as a basis for creating publication-ready papers
• To be aware of ‘continuous integration’ and ‘GitHub Actions’ and how they can be used to ensure reproducibility, share your work, and save time
• Understanding of best practices around code sharing and collaboration for reproducible research in transport planning

Prerequisites

This course assumes working knowledge with R or Python for research. We assume that you are already comfortable with an integrated development environment (IDE), such as RStudio or VS Code. You must have a GitHub account and it will be beneficial to be familiar with the concepts of version control, although we will cover these in the course.

Familiarity with referencing software such as Zotero (recommended) and bibliography file formats such as BibTeX will be beneficial, but not essential.

See the prerequisites page for details and to test your setup.

Questions for students (pre-course)

• What language would you prefer a course on reproducible research to be taught in?
  • R
  • Python
  • Both
• Which interactive development environment would you prefer to be used as the main editor used and taught during the course?
  • RStudio
  • VSCode
  • Positron (new data science-focussed IDE by Posit)

Day 1 (morning)

• 09:30-10:00 Introduction
  • Welcome and introductions (participatory)
  • Definitions and motivations
  • Course structure and objectives
• 10:00-11:00 Development environments, system commands, and version control
• 11:00-11:15 Break
• 11:15-12:30 Sharing code and data
• 12:30-13:30 Lunch

Day 1 (afternoon)

• 13:30-15:00 Reproducible papers and documentation with Quarto
  • Introduction to Quarto …
  • Practical: creating a minimal reproducible paper
• 15:00-15:15 Break
• 15:15-16:30 Cross-references and citations with Quarto
  • Cross-references
  • Citations
  • Bibliographies
  • Tables and figures
  • Practical: adding citations and references to your paper

Day 2 (morning)

• 09:30-10:30 Drafting a reproducible paper
  • Recap of Day 1
  • Topic selection
  • Individual work on paper drafts
• 10:30-10:45 Break
• 10:45-12:00 Generating reproducible publication-quality visualisations
  • An introduction to visualisation and web application development for transport planning
  • A deep dive into ggplot2
  • Practical: creating a visualisation for your paper
• 12:00-13:00 Lunch

Day 2 (afternoon)

• 13:00-14:30 Editing other people’s work
  • Reviewing and commenting on papers
  • Making changes and submitting Pull Requests
  • Controlled chaos: choose a paper and make some changes!
• 14:30-14:45 Break
• 14:45-16:00 Working on papers
  • Practical session bringing together elements from the course
• 16:00-17:00 Presentations and wrap-up

Practicalities

• Course website and open, reproducible code: tdscience.github.io/course/
• In person or online?
• Teaching assistants
• Number of participants
• Incorportating feedback
• Costs